This might enlighten you: Why you should use flatpaks over out-of-distribution repos
Also, I suggest that you install flatpaks as your user. To set that up:
flatpak --user remote-add --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo
flatpak --user remote-modify --enable flathub
That is all, from there on you can use Discover or GNOME Software to (un)install and update flatpaks
No.
That is not realy the case. There’s a number of things, like Cisco sponsoring us with the openh264 codecs, a lot of codecs no longer patented, so no problem to have in the distros.
Bumblebee is dead, but NVIDIA is something I do not have myself ( since ~15 years ), others might help you there.